Coexpression cluster:C4326

Full id: C4326_amniotic_H9_testicular_pancreatic_iPS_choriocarcinoma_signet

Phase1 CAGE Peaks

Hg19::chr3:32859521..32859546,+	p1@TRIM71
Hg19::chr7:100609304..100609322,+	p6@MUC3A p6@MUC3B
Hg19::chr7:100609327..100609376,+	p2@MUC3A p2@MUC3B

Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

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No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

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GO ID	GO name	FDR corrected p-value
GO:0005727	extrachromosomal circular DNA	0.000735900153067232
GO:0046821	extrachromosomal DNA	0.000735900153067232
GO:0030277	maintenance of gastrointestinal epithelium	0.00147175698093632
GO:0030197	extracellular matrix constituent, lubricant activity	0.00404685512039531
GO:0022600	digestive system process	0.00559135944153447
GO:0007586	digestion	0.0232712636788439
GO:0005201	extracellular matrix structural constituent	0.0258151955275526
GO:0032501	multicellular organismal process	0.0395447009256893

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>

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Cell Type

Ontology term	p-value	n
epithelial cell	2.22e-13	254
germ line cell	3.29e-08	7
germ cell	3.29e-08	7
endodermal cell	4.21e-07	59

Uber Anatomy

Ontology term	p-value	n
subdivision of digestive tract	7.61e-16	129
endodermal part of digestive tract	7.61e-16	129
endoderm-derived structure	1.57e-15	169
endoderm	1.57e-15	169
presumptive endoderm	1.57e-15	169
digestive system	1.55e-13	155
digestive tract	1.55e-13	155
primitive gut	1.55e-13	155
mixed endoderm/mesoderm-derived structure	1.98e-12	130
intestine	7.53e-10	27
gastrointestinal system	1.15e-09	35
foregut	1.23e-08	98
endo-epithelium	1.23e-08	82
trunk region element	1.73e-08	107
small intestine	2.77e-07	14
renal system	4.77e-07	45
immaterial anatomical entity	4.91e-07	126
larynx	6.41e-07	9
epithelial bud	7.50e-07	37

Disease

Ontology term	p-value	n
cell type cancer	2.97e-14	143
carcinoma	3.48e-14	106
disease of cellular proliferation	6.58e-09	239
cancer	1.54e-08	235

Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

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Novel motifs

JASPAR motifs

Motifs	-log10(p-value)
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ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
BCL3#602	2	23.0314018691589	0.00246467476084291	0.0138592670730454
NANOG#79923	2	19.4965189873418	0.00342725564850102	0.0174561888648524

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

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This analysis result is provided for C0 - C305 clusters.